[Dock-fans] Prepare Amber

[Rahul Banerjee]

Dear All,
 
I am trying to rescreen a set of ligand and rank them according to the Amber score. I am using prepare_amber.pl script (provided with Dock6). I found this program to be extremely slow (even slower than my dock6 run). Is it really the case or I am doing some thing wrong? Can I use multiple processors to run prepare_amber.pl ?

Also is there any limit on the number of ligands prepare_amber.pl can handle?

With best regards,

Rahul